Does blender have this tool : merge every vertices at certain distance point
It's called remove doubles and accessible through the Specials Menu: W > remove doubles. You can adjust the merge distance after applying the operation in the tools panel. 


Select the geometry in question (or all geometry with A).
Remove double through the W specials menu.
Adjust the merge distance if needed.




From the manual:


  Remove Doubles is a useful tool to simplify a mesh by merging the selected vertices that are closer than a specified distance to each other. An alternative way to simplify a mesh is to use the Decimate Modifier.


Using the decimate modifier will be not pay exceptional attention to the distance though and is in this case not useful.